– In 1944, an American and a Japanese pilot crash on an island in the South Pacific during World War II. The two engage in hand-to-hand combat, with the latter gaining the upper hand, before they are surprised by a large, ferocious creature.

28 years later, in 1973, former British Special Air Service Captain James Conrad is hired by government agent Bill Randa to guide an expedition to map out the island, known as „Skull Island”. Randa also recruits the Sky Devils, a helicopter squadron led by Lieutenant Colonel Preston Packard, to escort them to the island, and the group is soon joined by pacifist photojournalist Mason Weaver, who believes the scientific expedition to be a cover for a crooked military operation and plans to expose it.

Arriving on Skull Island, Packard’s men begin dropping explosives developed by seismologist Houston Brooks to determine if the ground is hollow, despite Conrad’s objections. The helicopters are suddenly attacked by a 100 foot-tall ape known as „Kong”, and many are destroyed, with the survivors split into two groups. The survivors’ only hope for rescue is a resupply team that will meet them at the island’s northern end in 3 days time. Packard confronts and threatens Randa, who reveals his affiliation to the secret government organization Monarch and the expedition’s true purpose: to acquire proof of the existence of monstrous creatures that have been forgotten by humanity in order to prepare for when these creatures return. Packard and his remaining men bury their dead comrades and begin searching for the missing members of the expedition, including Packard’s right-hand man, Major Jack Chapman. While trekking through the jungle, the men are attacked by a giant spider, killing one of them before Packard shoots it to death.

Meanwhile, Conrad, Weaver, Brooks, biologist San Lin, soldier Reg Slivko and Landsat employee Victor Nieves, among others, run into the local natives and meet Hank Marlow, who is revealed to be the missing pilot. Marlow explains that Kong is the island’s guardian and is worshipped as a god by the natives for protecting them from the Skullcrawlers, reptilian monsters that live underground and have slaughtered Kong’s ancestors, leaving him as the last of his kind. Marlow reveals Kong only attacked the helicopters to prevent the bombs from awakening the largest of the Skullcrawlers, the „Big One”. When informed of the pending rendezvous, Marlow says there is no possible way to reach it in time on foot, but luckily for the expedition, he has cobbled together a boat from the wreckage of his plane and is able to get it working with help from Conrad’s group.

Conrad’s group sets off down the river, where they are beset by pterosaur-like creatures, killing Nieves. The survivors manage to connect with Packard’s team, and while most wish to leave the island, Packard insists on searching for Chapman, who is still missing (unbeknownst to them, Chapman has already been ambushed and eaten by a Skullcrawler). Marlow reluctantly leads them to the Forbidden Zone, a forgotten battleground between Kong’s ancestors and Skullcrawlers. The same Skullcrawler that ate Chapman attacks the group, devouring Randa and killing many soldiers before they finally manage to bring the beast down. The creature inadvertently vomits up Chapman’s dog tags, allowing the team to deduce his fate. Packard blames Kong for the death of his men and retrieves explosives to lure Kong into a trap, while Conrad resolves to lead the non-military personnel back to the boat so they can rendezvous with the resupply team. While scouting the path ahead, Conrad and Weaver encounter Kong up-close and personal, and resolve to save him, a sentiment that Marlow shares. Packard’s trap successfully incapacitates Kong, and he orders his men to set explosives around the fallen creature, but before he can finish the ape off, Conrad’s group arrives and a standoff ensues. Conrad and Weaver convince the other soldiers to spare Kong, but Packard angrily refuses, and the group is suddenly attacked by the Big One, an Alpha Skullcrawler.

Packard stays behind as the others flee. Consumed with rage and his desire to avenge his dead comrades, he tries to detonate the explosives, but Kong recovers and crushes Packard before he can trigger the charges. An injured Kong is overpowered by the Alpha Skullcrawler, which then chases the survivors as they race towards the shore. Captain Earl Cole attempts to sacrifice himself to kill the pursuing Skullcrawler by arming grenades and allowing himself to be eaten, but the creature bats him away with its tail and corners the humans.

Kong returns to rescue them and, aided by the humans, he kills the Alpha Skullcrawler by ripping out its innards through the mouth. Weaver is violently thrown into a river by an explosion, but is then rescued by Kong. With the Skullcrawlers defeated, Kong allows the surviving humans to leave. Sometime afterward, Marlow returns home and is reunited with his wife and meets his son for the first time.

In a post-credits scene, Conrad and Weaver are detained by Monarch and informed by Brooks and Lin that Kong is not the only monster to roam the world. They are then shown archive footage of cave paintings depicting Godzilla, King Ghidorah, Rodan, and Mothra, with the last prophesizing Godzilla’s battle with King Ghidorah. As the scene fades, Godzilla’s roar is heard.